Design, synthesis, and biological evaluation of O-2-modified indenoisoquinolines as dual topoisomerase I-tyrosyl-DNA phosphodiesterase I inhibitors

Abstract

Tyrosyl-DNA phosphodiesterase I (TDP1) repairs stalled topoisomerase I (Top1)-DNA covalent complexes and has been proposed to be a promising and attractive target for cancer treatment. Inhibitors of TDP1 could conceivably act synergistically with Top1 inhibitors and thereby potentiate the effects of Top1 poisons. This study describes the successful design and synthesis of 2-position-modified indenoisoquinolines as dual Top1-TDP1 inhibitors using a structure-based drug design approach. Enzyme inhibition studies indicate that indenoisoquinolines modified at the 2-position with three-carbon side chains ending with amino substituents show both promising Top1 and TDP1 inhibitory activity. Molecular modeling of selected target compounds bound to Top1 and TDP1 was used to rationalize the enzyme inhibition results and structure-activity relationship analysis.

Scheme 1

Figure 1

Representative Top1 inhibitors.

Scheme 2

Figure 2

Representative TDP1 inhibitors.

Scheme 3

Figure 3

Hypothetical binding mode of compound 13 in a ternary complex with DNA and Top1. All distances are measured from heavy atom to heavy atom. The diagram is programmed for wall-eyed (relaxed) viewing. Compound 13 is shown in yellow sticks, and the base pairs are displayed in lines.

Scheme 4

Scheme 5

Scheme 6

Figure 4

Top1-mediated DNA cleavage induced by indenoisoquinolines 18, 19, and 21–23: lane 1, DNA alone; lane 2, Top1 + DNA; lane 3, 1 (1 μM); lane 4:, 5 (1 μM); lanes 5–24, 18, 19, 21, 22, and 23 (each at 0.1, 1, 10, and 100 μM from left to right). Numbers and arrows on the left indicate cleavage site positions.

Figure 5

Hypothetical binding mode of compound 20 in a ternary complex with DNA and Top1. All distances are measured from heavy atom to heavy atom. The diagram is programmed for wall-eyed (relaxed) viewing. Compound 20 is shown in pink sticks, and the base pairs are displayed in lines.

Scheme 7. Schematic Representation of the TDP1 Gel-Based Assays Using Recombinant TDP1

Figure 6

Representative gels showing concentration-dependent TDP1 inhibition by O-2-modified indenoisoquinolines 21, 18, 19, and 22: lane 1, DNA alone; lane 2, TDP1 + DNA; and lanes 3–22, 21, 18, 19, and 22 (each at 1.4, 4.1, 12.3, 37, and 111 μM from left to right).

Figure 7

Hypothetical binding mode of compound 22 in the active site of TDP1 (PDB ID: 1RFF). All distances are measured from heavy atom to heavy atom. The diagram is programmed for wall-eyed (relaxed) viewing. Compound 22 is shown in pink sticks.